Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022746.1 Corchorus olitorius cultivar O-4 contig22779, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 750
Length: 1250
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Found at i:934 original size:16 final size:16
Alignment explanation
Indices: 900--971 Score: 87
Period size: 16 Copynumber: 4.6 Consensus size: 16
890 CGGGCTCGGG
*
900 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
915 CGGGTT-GTGGTATTTT
1 CGGGTTCG-GGTATTTT
*
931 CGGGTTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
947 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
963 CGGGTTCGG
1 CGGGTTCGG
972 TCTCGGGTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
14 1 0.02
15 11 0.22
16 35 0.71
17 2 0.04
ACGTcount: A:0.06, C:0.14, G:0.42, T:0.39
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:959 original size:32 final size:31
Alignment explanation
Indices: 900--971 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 31
890 CGGGCTCGGG
900 CGGGTTCGGGTACTTCGGGTTGTGGTATTTT
1 CGGGTTCGGGTACTTCGGGTTGTGGTATTTT
931 CGGGTTCGGGTTA-TGTCGGGTTCG-GGTATTTT
1 CGGGTTCGGG-TACT-TCGGGTT-GTGGTATTTT
963 CGGGTTCGG
1 CGGGTTCGG
972 TCTCGGGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 11 0.29
32 26 0.68
33 1 0.03
ACGTcount: A:0.06, C:0.14, G:0.42, T:0.39
Consensus pattern (31 bp):
CGGGTTCGGGTACTTCGGGTTGTGGTATTTT
Found at i:970 original size:6 final size:6
Alignment explanation
Indices: 961--1043 Score: 102
Period size: 6 Copynumber: 14.3 Consensus size: 6
951 TTCGGGTATT
*
961 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCGGG TTCGGG -TCGGG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* *
1007 TTCGGG TTCGGG CTCGGG -TCGGG TTCGGG CTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TT
1044 TGATTTCGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
5 17 0.25
6 48 0.72
7 2 0.03
ACGTcount: A:0.01, C:0.19, G:0.49, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:994 original size:17 final size:18
Alignment explanation
Indices: 985--1043 Score: 104
Period size: 17 Copynumber: 3.4 Consensus size: 18
975 CGGGTAGGGT
985 TCGGGTTCGGGTTCGGG-
1 TCGGGTTCGGGTTCGGGC
1002 TCGGGTTCGGGTTCGGGC
1 TCGGGTTCGGGTTCGGGC
1020 TCGGG-TCGGGTTCGGGC
1 TCGGGTTCGGGTTCGGGC
1037 TCGGGTT
1 TCGGGTT
1044 TGATTTCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 34 0.85
18 6 0.15
ACGTcount: A:0.00, C:0.20, G:0.51, T:0.29
Consensus pattern (18 bp):
TCGGGTTCGGGTTCGGGC
Found at i:1041 original size:23 final size:23
Alignment explanation
Indices: 961--1041 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
951 TTCGGGTATT
* *
961 TTCGGGTTCGGTCTCGGGTAGGG
1 TTCGGGTTCGGGCTCGGGTCGGG
*
984 TTCGGGTTCGGGTTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGGTCGGG
1007 TTCGGGTTCGGGCTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGGTCGGG
*
1030 TTCGGGCTCGGG
1 TTCGGGTTCGGG
1042 TTTGATTTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.01, C:0.20, G:0.51, T:0.28
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCGGGTCGGG
Found at i:1176 original size:8 final size:8
Alignment explanation
Indices: 1156--1189 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
1146 AAGTTTATTT
1156 ATAATAT-
1 ATAATATA
1163 ATAATATA
1 ATAATATA
1171 ATAATATA
1 ATAATATA
1179 ATAATATA
1 ATAATATA
1187 ATA
1 ATA
1190 TAACATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:1179 original size:13 final size:13
Alignment explanation
Indices: 1155--1192 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1145 TAAGTTTATT
1155 TATAAT-ATATAA
1 TATAATAATATAA
1167 TATAATAATATAA
1 TATAATAATATAA
1180 TA-ATATAATATAA
1 TATA-ATAATATAA
1193 CATTATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAATAATATAA
Done.